From b92018c59766736b1958428c61e6caf56712ad05 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?L=C3=A9o=20Gaspard?= <nehzio@morgoth.lan>
Date: Wed, 17 Feb 2021 13:22:20 +0100
Subject: [PATCH] fixed symmetry

---
 DOC.md         |  4 ++++
 crystal_met.py | 16 +++++++++-------
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/DOC.md b/DOC.md
index 52efd57..61387a1 100644
--- a/DOC.md
+++ b/DOC.md
@@ -104,3 +104,7 @@ Will use an optimization method to set the total charge to 0 by slightly changin
 
 Simili Evjen method to calculate the charge of the atom on the outer shell, note that OPTIMIZATION and EVJEN keywords can not be used together
 
+* SYMMETRY [C2x C2y C2z xOy xOz yOz i]
+
+Symmetry operations in the fragment and bath to be applied to everyhing
+
diff --git a/crystal_met.py b/crystal_met.py
index 71d95a2..676e744 100644
--- a/crystal_met.py
+++ b/crystal_met.py
@@ -431,7 +431,7 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
             if name == atoms[index]:  #Check if it is the same atom
                 if distance(t,a) == 0:
                     print("ERROR : Twice the same atom")
-                if 'xOz' in operations:
+                if np.abs(a[1]) > da and 'xOz' in operations:
                     if distance(t,d) <= da:
                         newCoord.append(d)
                         newCoord[-1].append(name+'d')
@@ -443,7 +443,7 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
                         print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
                         print("Are you sure about the xOz symmetry operation ?")
                         break
-                if 'yOz' in operations:
+                if np.abs(a[0]) > da and 'yOz' in operations:
                     if distance(t,b) <= da:
                         newCoord.append(b)
                         newCoord[-1].append(name+'b')
@@ -455,7 +455,7 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
                         print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
                         print("Are you sure about the yOz symmetry operation ?")
                         break
-                if 'C2z' in operations:
+                if (np.abs(a[0]) > da and np.abs(a[1]) > da) and 'C2z' in operations:
                     if distance(t,c) <= da:
                         newCoord.append(c)
                         newCoord[-1].append(name+'c')
@@ -467,7 +467,7 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
                         print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
                         print("Are you sure about the C2z symmetry operation ?")
                         break
-                if 'xOy' in operations:
+                if np.abs(a[2]) > da and 'xOy' in operations:
                     if distance(t,e) <= da:
                         newCoord.append(e)
                         newCoord[-1].append(name+'e')
@@ -479,7 +479,7 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
                         print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
                         print("Are you sure about the xOy symmetry operation ?")
                         break
-                if 'C2y' in operations:
+                if (np.abs(a[0]) > da and np.abs(a[2]) > da) and 'C2y' in operations:
                     if distance(t,f) <= da:
                         newCoord.append(f)
                         newCoord[-1].append(name+'f')
@@ -491,7 +491,7 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
                         print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
                         print("Are you sure about the C2y symmetry operation ?")
                         break
-                if 'C2x' in operations:
+                if (np.abs(a[1]) > da and np.abs(a[2]) > da) and 'C2x' in operations:
                     if distance(t,g) <= da:
                         newCoord.append(g)
                         newCoord[-1].append(name+'g')
@@ -503,7 +503,7 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
                         print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
                         print("Are you sure about the C2x symmetry operation ?")
                         break
-                if 'i' in operations:
+                if (np.abs(a[0]) > da and np.abs(a[1]) > da and np.abs(a[2]) > da) and 'i' in operations:
                     if distance(t,h) <= da:
                         newCoord.append(h)
                         newCoord[-1].append(name+'h')
@@ -836,6 +836,8 @@ def main():
                     prog += 1
                     now = datetime.datetime.now()
                     printProgressBar(start,now,prog,((len(coords)-1)*len(coords))/2,prefix='Calculating nuclear repulsion',length=50)
+                    if(distance(coords[i],coords[j])<=da):
+                        print(i,j,coords[i],coords[j])
                     rep += (coords[i][4]*coords[j][4])/distance(coords[i],coords[j])
             print("Nuclear repulsion after symmetry : %f"%rep)
     else: